Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CBX3

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF7 cells
cell line
MCF7
cell type
human breast cancer cells
treatment
E2_14h
antibody
Millipore 05-690 (Lot#3224566)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% formaldehyde at room temperature for 10 min. And then the cross-linking was quenched with 0.125M glycine for 5 min. Chromatin was fragmented using a Bioruptor® Pico (Diagenode) for 10 min at high power, with an interval of 30 s between pulses to get around 200bp fragments and precleared using 20 μl Protein G Dynabeads (Life Technologies, Cat# 10009D). Subsequently, the soluble chromatin was incubated with 2-5 μg antibodies at 4°C overnight. Immunoprecipitated complexes were collected using 30 μl Protein G Dynabeads, which have been saturated with PBS/1% BSA over night at 4°C, per reaction. For all ChIPs, after de-crosslinking overnight at 65°C, final ChIP DNA was extracted and purified using QIAquick spin columns (QIAGEN). The libraries were constructed following Illumina's Chip-Seq Sample prep kit.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
34181190
Reads aligned (%)
71.3
Duplicates removed (%)
12.2
Number of peaks
1348 (qval < 1E-05)

hg19

Number of total reads
34181190
Reads aligned (%)
70.7
Duplicates removed (%)
12.6
Number of peaks
563 (qval < 1E-05)

Base call quality data from DBCLS SRA